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Well, the "and then stop" part is easy..
The remainder can be done in a manner similar to the DCS Loader when it is controlling the TIU over a USB emulated RS-232 for sound file transfer, etc. The external microcontroller would have to unlock the interface (a small Speck of code for this) and send a sequence of ASCII commands to set whatever settings you want to set.
Its my experience on original TIU, that the radio and the 9-pin DB can function at the same time.
@Adrian! posted:STORY: In our club, the Flash memory is starting to go on the TIUs, and they are forgetting some of their settings (Fixed vs Variable, Outputs On vs. Off) on every power cycle. Replacing the Flash on the PCB is a world class pain (I tried one) , 1) it's obsolete and hard to find and 2) basically a lead-less package that is not rework friendly.
I certainly agree that replacing that FLASH would be a PITA. I'm curious, what you think is causing the multiple failures of the FLASH? Since I haven't really seen that personally, I wonder what is exclusive about SOCAL that is killing your FLASH chips. 
We're rough on everything (lots of power cycles per hour).
We have 5 TIUs in the layout, but only two of them are doing this, and they are the ones where 95% of turnouts and derailments are. The other 3 that are fine cover mostly straights runs that don't see much excitement.
Having thought about this for awhile, I suggest a different approach.
I would assemble an ESP8266 and a radio. Write a sketch that that sends the appropriate commands out over the radio to each of the 5 TIU "and then stop".
